BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 880,933 number of mapped reads = 811,948 (92.17%) number of supplementary alignments = 4,562 (0.52%) number of secondary alignments = 0 number of mapped bases = 47,594,135 bp number of sequenced bases = 47,579,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,390 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1341 >>>>>>> ACTG content number of A's = 11,824,747 bp (24.85%) number of C's = 8,704,723 bp (18.3%) number of T's = 15,407,827 bp (32.38%) number of G's = 11,636,189 bp (24.46%) number of N's = 6,222 bp (0.01%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 230,776 number of insertions = 3,352 mapped reads with insertion percentage = 0.41% number of deletions = 9,173 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1733X There is a 1.44% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3973592 0.015942154864280158 0.2973213675595489 chr2 243199373 3074510 0.012641932263534248 0.1706536428887526 chr3 198022430 3444362 0.017393797258219688 0.13702656068931468 chr4 191154276 2598720 0.013594882910178793 0.12580736515116928 chr5 180915260 2895126 0.01600266334636448 0.13173755632894893 chr6 171115067 3094500 0.018084322171349178 0.14666333256803413 chr7 159138663 2177276 0.013681628078024005 0.22205680492130755 chr8 146364022 5191220 0.0354678692827941 0.24339755043803252 chr9 141213431 1954039 0.013837486888906481 0.14857036585541328 chr10 135534747 2358267 0.017399722596597313 0.1684035355547998 chr11 135006516 2280211 0.01688963664538977 0.15805664466020647 chr12 133851895 1884656 0.014080159268570685 0.1242871304751647 chr13 115169878 1233874 0.010713513128840859 0.10733889709736796 chr14 107349540 1003962 0.009352271094966965 0.10565830732600598 chr15 102531392 1429611 0.013943154112254713 0.12330073079159493 chr16 90354753 1363126 0.015086378466443265 0.134240836505472 chr17 81195210 1292163 0.01591427622392996 0.14016056189333703 chr18 78077248 1159040 0.014844785512932014 0.2456005166479017 chr19 59128983 681686 0.011528796292674271 0.22440072166990335 chr20 63025520 976260 0.015489915830920555 0.13014870647491175 chr21 48129895 630773 0.013105638397922954 0.12348020591974924 chr22 51304566 279550 0.005448832760811192 0.07601352310115186 chrMT 16571 105475 6.365035302637137 4.0218634327742775 chrX 155270560 2392159 0.015406391269536222 0.1405114156334733 chrY 59373566 119977 0.0020207140665932043 0.05899064632139315